Index _ | A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | W _ __init__() (papylio.Experiment method) (papylio.File method) (papylio.Movie method) A absoluteFilePath (papylio.File property) add_common_image_corrections_to_movies() (papylio.Experiment method) add_extensions() (papylio.File method) add_files() (papylio.Experiment method) analysis_path (papylio.Experiment property) analyze_dwells() (in module papylio.analysis.dwell_time_analysis) (papylio.File method) apply_classifications() (papylio.File method) apply_corrections() (papylio.Movie method) apply_selections() (papylio.File method) apply_trace_corrections() (papylio.File method) auto_bin_size_for_discrete_data() (in module papylio.analysis.dwell_time_analysis) autoThreshold() (papylio.File method) average_image() (papylio.File method) B BIC() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) BIC_histogram() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) bitdepth (papylio.Movie property) boundaries_metric (papylio.Movie property) boundaries_stage (papylio.Movie property) boxplot_number_of_molecules() (papylio.Experiment method) bytes_per_frame (papylio.Movie property) C calculate_FRET() (papylio.File method) cdf() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) cdf_fit() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) cdf_untruncated() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) channel_arrangement (papylio.Movie property) channel_columns (papylio.Movie property) channel_indices (papylio.Movie property) channel_rows (papylio.Movie property) channels (papylio.Experiment property) classification (papylio.File property) classification_binary() (papylio.File method) classification_configurations() (papylio.File method) classification_names (papylio.File property) classifications (papylio.File property) classify_hmm() (papylio.File method) clear_classifications() (papylio.File method) clear_selections() (papylio.File method) configuration (papylio.File property) (papylio.Movie property) coordinates (papylio.File property) coordinates_from_channel() (papylio.File method) coordinates_metric (papylio.File property) coordinates_stage (papylio.File property) copy_coordinates_to_selected_files() (papylio.File method) copy_selections_to_selected_files() (papylio.File method) corrections (papylio.Movie property) corrections_filepath (papylio.Movie property) create_classification() (papylio.File method) create_selection() (papylio.File method) cycle_time (papylio.File property) D data_type (papylio.Movie property) data_vars (papylio.File property) dataset (papylio.File property) dataset_attributes (papylio.File property) dataset_selected (papylio.File property) dataset_to_parameters() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) determine_dwells_from_classification() (papylio.File method) determine_flatfield_and_darkfield_corrections() (papylio.Experiment method) determine_general_background_correction() (papylio.Movie method) determine_psf_size() (papylio.File method) determine_sequences_at_current_coordinates() (papylio.File method) determine_spatial_background_correction() (papylio.Movie method) determine_temporal_background_correction() (papylio.Movie method) determine_trace_correction() (papylio.File method) dwell_analysis (papylio.File property) dwells (papylio.File property) E empirical_cdf() (in module papylio.analysis.dwell_time_analysis) Experiment (class in papylio) ExponentialDistribution (class in papylio.analysis.dwell_time_analysis) export_coeff_file() (papylio.File method) export_map_file() (papylio.File method) export_mapping() (papylio.File method) export_number_of_molecules_per_file() (papylio.Experiment method) export_pks_file() (papylio.File method) export_sequencing_match() (papylio.File method) export_traces_file() (papylio.File method) extract_background() (papylio.File method) extract_traces() (papylio.File method) F File (class in papylio) file_paths (papylio.Experiment property) files_with_sequencing_match() (papylio.Experiment method) find_and_add_extensions() (papylio.File method) find_coordinates() (papylio.File method) find_extensions() (papylio.File method) find_file_paths_and_extensions() (papylio.Experiment method) find_sequences_using_stage_coordinates() (papylio.File method) fit_dwell_times() (in module papylio.analysis.dwell_time_analysis) flatten_channels() (papylio.Movie method) frame_indices (papylio.Movie property) frame_rate (papylio.File property) frames_to_xarray_dataarray() (papylio.Movie method) G generate_sequencing_match() (papylio.File method) generate_tile_mappings() (papylio.Experiment method) get_channel() (papylio.Movie method) get_channel_from_name() (papylio.Movie method) get_channel_indices_from_names() (papylio.Movie method) get_channels_from_names() (papylio.Movie method) get_data() (papylio.File method) get_dataset_attribute() (papylio.File method) get_illumination_from_name() (papylio.Movie class method) get_illumination_indices_from_names() (papylio.Movie class method) get_illuminations_from_names() (papylio.Movie class method) get_projection_image() (papylio.File method) get_sequencing_data() (papylio.File method) get_traces() (papylio.File method) get_variable() (papylio.File method) H has_sequencing_match (papylio.File property) height_metric (papylio.Movie property) hist_fit() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) histogram() (papylio.Experiment method) histogram_2D_FRET_intensity_total() (papylio.File method) histogram_2D_intensity_per_channel() (papylio.File method) histogram_fit() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) I illumination_arrangement (papylio.Movie property) illumination_index_per_frame (papylio.Movie property) illumination_indices (papylio.Movie property) illumination_indices_in_movie (papylio.Movie property) illuminations (papylio.Movie attribute) image_info_from_filename() (papylio.Movie class method) image_info_to_filename() (papylio.Movie class method) import_coeff_file() (papylio.File method) import_excel_file() (papylio.File method) import_map_file() (papylio.File method) import_mapping_file() (papylio.File method) import_movie() (papylio.File method) import_pks_file() (papylio.File method) import_sequencing_data() (papylio.Experiment method) import_sequencing_data_for_mapping() (papylio.Experiment method) import_sequencing_data_old() (papylio.Experiment method) import_sequencing_match() (papylio.File method) import_traces_file() (papylio.File method) insert_sequencing_data_into_file_dataset() (papylio.File method) intensity_total (papylio.File property) L likelihood() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) load_darkfield_correction() (papylio.Experiment method) load_flatfield_correction() (papylio.Experiment method) loglikelihood() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) loglikelihood_binned() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) M make_average_image() (papylio.Movie method) make_maximum_projection() (papylio.Movie method) make_projection_image() (papylio.Movie method) make_projection_images() (papylio.Movie method) mapping_file (papylio.Experiment property) maximum_likelihood_estimation() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) maximum_projection_image() (papylio.File method) mle() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) module papylio.analysis.dwell_time_analysis Movie (class in papylio) N nc_file_paths (papylio.Experiment property) negative_loglikelihood() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) negative_loglikelihood_binned() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) noneFunction() (papylio.File method) number_of_channels (papylio.Experiment property) (papylio.File property) (papylio.Movie property) number_of_channels_per_frame (papylio.Movie property) number_of_illuminations (papylio.Movie property) number_of_illuminations_in_movie (papylio.Movie property) number_of_molecules (papylio.File property) number_of_selected_molecules (papylio.File property) number_of_states_from_classification (papylio.File property) P P_and_k_from_parameters() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) pairs (papylio.Experiment property) papylio.analysis.dwell_time_analysis module parameter_guess() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) parameter_names (papylio.analysis.dwell_time_analysis.ExponentialDistribution property) parameter_names_full (papylio.analysis.dwell_time_analysis.ExponentialDistribution property) parameters_full() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) parameters_to_dataset() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) pdf() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) pdf_binned() (papylio.analysis.dwell_time_analysis.ExponentialDistribution method) perform_mapping() (papylio.File method) pixel_to_stage_coordinates_transformation (papylio.Movie property) pixels_per_frame (papylio.Movie property) plot_dwell_analysis() (in module papylio.analysis.dwell_time_analysis) (papylio.File method) plot_dwell_analysis_state() (in module papylio.analysis.dwell_time_analysis) plot_dwell_time_histogram() (in module papylio.analysis.dwell_time_analysis) plot_empirical_cdf() (in module papylio.analysis.dwell_time_analysis) plot_hmm_rates() (papylio.File method) plot_sequencing_match() (papylio.File method) plot_trace() (papylio.Experiment method) print_files() (papylio.Experiment method) projection_image() (papylio.File method) R read_frame() (papylio.Movie method) read_frames() (papylio.Movie method) read_header() (papylio.Movie method) relativeFilePath (papylio.File property) reset_corrections() (papylio.Movie method) S sampling_interval (papylio.File property) save_corrections() (papylio.Movie method) save_dataset_selected() (papylio.File method) saveas_tif() (papylio.Movie method) savetoExcel() (papylio.File method) select() (papylio.Experiment method) selected_molecules (papylio.File property) selectedFiles (papylio.Experiment property) selection_configurations() (papylio.File method) selection_names (papylio.File property) selection_names_active (papylio.File property) selections (papylio.File property) separate_channels() (papylio.Movie method) sequencing_data (papylio.File property) sequencing_match (papylio.File property) sequencing_match_info_mean() (papylio.Experiment method) sequencing_match_info_per_file() (papylio.Experiment method) sequencing_matches() (papylio.Experiment method) set_coordinates_of_channel() (papylio.File method) set_variable() (papylio.File method) show() (papylio.Movie method) show_average_image() (papylio.File method) show_coordinates() (papylio.File method) show_coordinates_in_image() (papylio.File method) show_correction() (papylio.Movie method) show_histogram() (papylio.File method) show_image() (papylio.File method) show_mapping_in_image() (papylio.File method) show_sequencing_matches() (papylio.Experiment method) show_traces() (papylio.File method) state_count() (papylio.File method) state_fraction() (papylio.File method) T tile_mappings (papylio.Experiment property) tile_mappings_dict (papylio.Experiment property) time (papylio.Movie property) traces_names (papylio.File property) transform_sequencing_to_single_molecule_coordinates() (papylio.Experiment method) type_dict() (papylio.Movie class method) U use_for_darkfield_correction() (papylio.File method) use_mapping_for_all_files() (papylio.File method) use_sequences_as_molecules() (papylio.File method) W width_metric (papylio.Movie property)
